Orientation

structure.pdb.orientation.cli_minimize_box()

Command-line interface for rotating protein to minimize box volume.

structure.pdb.orientation.minimize_box(positions)

Rotate system to minimize box size.

PARAMETER	DESCRIPTION
positions	Cartesian coordinates of system. TYPE: NDArray[float64]

RETURNS	DESCRIPTION
NDArray[float64]	Optimized positions with minimal box size.

structure.pdb.orientation.rotate_positions(positions, rotation_v)

structure.pdb.orientation.run_minimize_box(pdb_path, output_path=None)

Minimize box size by rotating protein.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file. TYPE: str
output_path	Path to save new PDB file. If None, then no file is written. TYPE: str | None DEFAULT: None

RETURNS	DESCRIPTION
NDArray[float64]	Atomic positions rotated to minimum box volume.

structure.pdb.orientation.volume_objective_f(rotation_v, positions)

Objective function that returns box volume